Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP025268	2,997,537	(A)8→7	intergenic (‑140/+83)	CXP41_RS15625 ← / ← CXP41_RS24400	response regulator transcription factor/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP025268	2,997,530	0	A	.	100.0%	139.7 / NA	30	intergenic (‑133/+90)	CXP41_RS15625/CXP41_RS24400	response regulator transcription factor/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (12/18);  total (12/18)

TATATTCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAAT  >  NZ_CP025268/2997397‑2997651                                                                                                                                      |                                                                                                                          tatatTCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTaaaaaaa                                                                                                                     <  1:2447288/140‑1 (MQ=255)          ccTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAgg                                                                                                           <  2:2438453/140‑1 (MQ=255)              aGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCAtt                                                                                                       >  2:3591442/1‑140 (MQ=255)              aGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACAGTGATGAAATAATAATGAAATTTAATTAAAAATAAAATTTTTGCGT‑AAATAAATACCACAGGCAtt                                                                                                       >  2:7733740/1‑140 (MQ=255)                tgtAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTaa                                                                                                     >  2:3463464/1‑140 (MQ=255)                 gtAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTaaa                                                                                                    <  1:10755630/140‑1 (MQ=255)                 gtAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTaaa                                                                                                    <  2:7116891/140‑1 (MQ=255)                           tAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATgag                                                                                          <  2:8120514/140‑1 (MQ=255)                                cattcattTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAgatgat                                                                                     <  2:5654661/140‑1 (MQ=255)                                  ttcattTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCAGTAAAAAATCATGAGATGATTa                                                                                   >  1:9600112/1‑140 (MQ=255)                                   tcattTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTaa                                                                                  >  1:2522633/1‑140 (MQ=255)                                          taATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTa                                                                           <  2:11059352/140‑1 (MQ=255)                                             tcatcCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACaa                                                                        <  1:9738135/140‑1 (MQ=255)                                               atcCCTTCCATTATTATTATAAGCAAAATCGAAAGAATACATTGATGAATTAATAATGAATTATATTTAAAAATTAAATTTTTTCGT‑AAAAATTTACCACAGGATTTATAAAATCATGTGATGATTATTATATTACAAtt                                                                      <  2:2855482/140‑1 (MQ=255)                                               atcCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAACTATTACAAtt                                                                      <  2:9297850/140‑1 (MQ=255)                                                tcCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATgag                                                                                          <  1:8846109/119‑1 (MQ=255)                                                tcCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATgag                                                                                          >  2:8846109/1‑119 (MQ=255)                                                            ttattatAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTATAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCaa                                                         <  2:1716877/140‑1 (MQ=255)                                                            ttattatAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCaa                                                         <  1:3066177/140‑1 (MQ=255)                                                                 ataAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCAt                                                    >  1:1228811/1‑140 (MQ=255)                                                                  taAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCAtt                                                   >  1:5564646/1‑140 (MQ=255)                                                                                 gactACATTGATGAAATAATAATGAAATATAAATAAAAATAAAATTTTTGCGT‑AAAAAAATACCACATGCATTAAAAAATCATGAGATGATTAAAATAGTACAATTAGATTATATTCTAATCATTAAACTTGAGCCAggg                                    <  2:8837039/137‑1 (MQ=255)                                                                                         tgatgaAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATaa                            <  2:3185305/140‑1 (MQ=255)                                                                                          gatgaAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAACAATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAg                           >  2:545968/1‑140 (MQ=255)                                                                                           atgaAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGt                          >  2:286924/1‑140 (MQ=255)                                                                                           atgaAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGt                          >  2:286876/1‑140 (MQ=255)                                                                                              aaaTAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCt                       >  1:5893113/1‑140 (MQ=255)                                                                                                   ataatGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAggg                  <  2:3263117/140‑1 (MQ=255)                                                                                                     aatGAAATATAATTAAAAATAAACTTTTTGCGT‑ACAAAAATACCACAGGCATTAAAAAATCATGAGAGGATTAACCTATTACCATGAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCt                <  2:5735023/140‑1 (MQ=255)                                                                                                             ataATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCaaaa        <  2:4570331/140‑1 (MQ=255)                                                                                                                   aaaaaTAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAat  <  2:1228811/140‑1 (MQ=255)                                                                                                                                      |                                                                                                                          TATATTCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAAT  >  NZ_CP025268/2997397‑2997651

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑